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- PDB-6g1j: Phosphotriesterase PTE_C23M_1 -

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Basic information

Entry
Database: PDB / ID: 6g1j
TitlePhosphotriesterase PTE_C23M_1
ComponentsParathion hydrolase
KeywordsHYDROLASE / Metalloenzyme / TIM barrel
Function / homology
Function and homology information


aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding / plasma membrane
Similarity search - Function
Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel ...Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1-ethyl-1-methyl-cyclohexane / FORMIC ACID / IMIDAZOLE / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDym, O. / Aggarwal, N. / Albeck, S. / Unger, T. / Hamer Rogotner, S. / Silman, I. / Leader, H. / Ashani, Y. / Goldsmith, M. / Greisen, P. ...Dym, O. / Aggarwal, N. / Albeck, S. / Unger, T. / Hamer Rogotner, S. / Silman, I. / Leader, H. / Ashani, Y. / Goldsmith, M. / Greisen, P. / Tawfik, D. / Sussman, L.J.
CitationJournal: To Be Published
Title: Phosphotriesterase PTE_C23M_1
Authors: Dym, O. / Aggarwal, N. / Albeck, S. / Unger, T. / Hamer Rogotner, S. / Silman, I. / Leader, H. / Ashani, Y. / Goldsmith, M. / Greisen, P. / Tawfik, D. / Sussman, L.J.
History
DepositionMar 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,99415
Polymers35,8351
Non-polymers1,16014
Water3,207178
1
A: Parathion hydrolase
hetero molecules

A: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,98830
Polymers71,6692
Non-polymers2,31928
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7570 Å2
ΔGint-316 kcal/mol
Surface area22840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.670, 69.670, 186.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-665-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Parathion hydrolase / Phosphotriesterase / PTE


Mass: 35834.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Gene: opd / Production host: Escherichia coli (E. coli) / References: UniProt: P0A434, aryldialkylphosphatase

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Non-polymers , 7 types, 192 molecules

#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-E8N / 1-ethyl-1-methyl-cyclohexane


Mass: 126.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H18
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Tris pH=7 1.5M (NH4)2SO4 17% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.1→29.73 Å / Num. obs: 27715 / % possible obs: 99.93 % / Redundancy: 20 % / Biso Wilson estimate: 18.42 Å2 / Rmerge(I) obs: 0.02175 / Net I/σ(I): 25.28
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 15 % / Rmerge(I) obs: 0.07357 / Mean I/σ(I) obs: 10.18 / Num. unique obs: 2707 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HYZ

1hyz


Resolution: 2.1→29.7 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.982 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20101 1401 5.1 %RANDOM
Rwork0.16379 ---
obs0.16569 26314 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.127 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0 Å2-0 Å2
2--0.5 Å20 Å2
3----1 Å2
Refinement stepCycle: 1 / Resolution: 2.1→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 60 178 2736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192634
X-RAY DIFFRACTIONr_bond_other_d0.0030.022497
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.9793571
X-RAY DIFFRACTIONr_angle_other_deg1.1463.0045740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8375338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82122.286105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.21415416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0531526
X-RAY DIFFRACTIONr_chiral_restr0.1160.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212924
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02554
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5681.7431340
X-RAY DIFFRACTIONr_mcbond_other1.5681.7431341
X-RAY DIFFRACTIONr_mcangle_it2.312.5951679
X-RAY DIFFRACTIONr_mcangle_other2.312.5981680
X-RAY DIFFRACTIONr_scbond_it2.6972.0471294
X-RAY DIFFRACTIONr_scbond_other2.6382.0311291
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7632.9451886
X-RAY DIFFRACTIONr_long_range_B_refined5.40421.8153014
X-RAY DIFFRACTIONr_long_range_B_other5.33121.6922978
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 98 -
Rwork0.168 1899 -
obs--100 %

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